2JIR

A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005506	molecular_function	iron ion binding
A	0006777	biological_process	Mo-molybdopterin cofactor biosynthetic process
A	0008940	molecular_function	nitrate reductase activity
A	0009055	molecular_function	electron transfer activity
A	0009325	cellular_component	nitrate reductase complex
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0030151	molecular_function	molybdenum ion binding
A	0042128	biological_process	nitrate assimilation
A	0042597	cellular_component	periplasmic space
A	0043546	molecular_function	molybdopterin cofactor binding
A	0045333	biological_process	cellular respiration
A	0046872	molecular_function	metal ion binding
A	0050140	molecular_function	nitrate reductase (cytochrome) activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 A 800

Chain	Residue
A	CYS13
A	TYR15
A	CYS16
A	GLY19
A	CYS20
A	CYS47
A	PRO182
A	VAL183

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MO A 810

Chain	Residue
A	MGD811
A	MGD812
A	CYN813
A	CYS140

---

site_id	AC3
Number of Residues	32
Details	BINDING SITE FOR RESIDUE MGD A 811

Chain	Residue
A	ARG14
A	GLN111
A	ASN136
A	CYS140
A	GLN312
A	GLN346
A	GLU416
A	THR417
A	ASN418
A	THR422
A	ILE443
A	GLU444
A	ALA445
A	PHE446
A	PRO461
A	ALA462
A	PHE463
A	SER615
A	ARG617
A	TRP622
A	HIS623
A	THR624
A	THR626
A	PHE689
A	ASN697
A	TYR713
A	LYS714
A	MO810
A	MGD812
A	CYN813
A	HOH2478
A	HOH2588

---

site_id	AC4
Number of Residues	38
Details	BINDING SITE FOR RESIDUE MGD A 812

Chain	Residue
A	CYS16
A	LYS49
A	CYS140
A	ILE173
A	GLY174
A	SER175
A	ASN176
A	GLU179
A	ALA180
A	ASP204
A	PRO205
A	ARG206
A	PHE220
A	PRO222
A	GLY223
A	ASP225
A	CYS307
A	MET308
A	GLY309
A	ARG313
A	GLY345
A	GLN346
A	THR614
A	MET616
A	ARG617
A	VAL618
A	ILE619
A	HIS621
A	TRP622
A	HIS623
A	LYS714
A	MO810
A	MGD811
A	CYN813
A	HOH2196
A	HOH2199
A	HOH2664
A	HOH2669

---

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CYN A 813

Chain	Residue
A	CYS140
A	MET141
A	GLN346
A	ALA349
A	MO810
A	MGD811
A	MGD812

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NO2 A 814

Chain	Residue
A	MET616
A	ARG617
A	VAL618
A	HIS621
A	PHE689

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	55
Details	Domain: {"description":"4Fe-4S Mo/W bis-MGD-type","evidences":[{"source":"HAMAP-Rule","id":"MF_01630","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	22
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01630","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10368307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18327621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2JIM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2NAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V3V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V45","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01630","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10368307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18327621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2JIM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2NAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V3V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V45","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10368307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18327621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2JIM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2NAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V3V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V45","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01630","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10368307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18327621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2JIM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2NAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V3V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V45","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	5
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18327621","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2JIQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01630","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"18327621","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2JIQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2JIR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1tmo

Chain	Residue	Details
A	CYS140

---

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1tmo

Chain	Residue	Details
A	ARG138

---